Read community sequences

There are two OTU tables and I named them arbitrarily:

  1. communities_abundance: raw data from Nanxi
  2. communities_abundance_syl: curated community ESV table from Sylvie

I formated the data.frame so that both of them have the following variables:

In communities_abundance_syl, there are other parameters

communities_abundance_syl

Community richness along transfers based on communities_abundance

Match community ESVs and isolate Sanger sequences

Save the alignment result

IUPAC notation for DNA base pairs

W, S, M, K, R, Y represent two possiblities for one base pair B, D, H, V represent three possiblitieis N means any nucleotide (but not a gap)

I tested five alignment methods in Biostrings::pairwiseAlignment()

[1] "global"       "local"        "overlap"      "global-local" "local-global"

Number of isolates being matched to the community ESV if we allow for up to two mismatches.

Up to one mistmatch

No mistmatch

Relative abundance explained by the sequences

Abundances explained by ESVs

Abundances explained by ESVs in 13 communties

Abundance explained by isolate sequences, allowing up to two mismatch. C2R6 and C10R2 both miss one isolate’s Sanger sequences.

Abundance explained by isolate sequences. Rows are different alignment algorithms used by Biostring::pairwiseAlignment(), whereas columns are how many bp mismatches are allowed in ESV-Sanger matches.

---
title: "Sequence abundances in community"
author: "Chang-Yu Chang"
date: "`r Sys.Date()`"
output:
  html_notebook:
    number_sections: no
    toc: yes
  bookdown::pdf_document2:
    number_sections: no
    toc: no
  html_document:
    df_print: paged
    toc: yes
  pdf_document:
    toc: yes
linkcolor: red
fontsize: 12pt
urlcolor: blue
---

```{r setup, include = FALSE}
# Knitr options
knitr::opts_chunk$set(
  cache = TRUE,
  echo = FALSE,
  fig.align = "center",
  fig.height = 4,
  fig.width = 6)

# Library
library(tidyverse)
library(data.table)
library(invnet)

# Local directory and functions
root <- rprojroot::is_r_package # Package root
source(root$find_file("misc/utils.R"))
source(root$find_file("misc/sequence_pairwise_alignment.R"))
write_all_csv <- TRUE
write_all_pdf <- TRUE

# Parameters 
isolates_ID_match <- fread(root$find_file("data/temp/isolates_ID_match.csv"))
communities <- fread(root$find_file("data/temp/communities.csv"))
communities_name <- communities$Community
communities_size <- communities$CommunitySize
communities_name_pool <- c(paste0("C", 1:12, "Rpool"), paste0("C", rep(1:12, each = 8), "R", rep(1:8, 12)))
families_name <- c("Aeromonadaceae", "Alcaligenaceae", "Bradyrhizobiaceae", "Brucellaceae", "Burkholderiaceae", "Caulobacteraceae", "Cellulomonadaceae", "Chitinophagaceae", "Chthoniobacteraceae", "Comamonadaceae", "Cryomorphaceae", "Enterobacteriaceae", "Enterococcaceae", "Flavobacteriaceae", "Hyphomicrobiaceae", "Listeriaceae", "Microbacteriaceae", "Moraxellaceae", "Nocardiaceae", "Obscuribacterales.17", "Oxalobacteraceae", "Paenibacillaceae", "Phyllobacteriaceae", "Porphyromonadaceae", "Pseudomonadaceae", "Rhizobiaceae", "Sanguibacteraceae", "Sphingobacteriaceae", "Sphingomonadaceae", "Xanthomonadaceae")
```


# Read community sequences

```{r}
source("script/01E-match_community_abundance-01-community_sequence.R")
```

There are two OTU tables and I named them arbitrarily:

1. `communities_abundance`: raw data from Nanxi
2. `communities_abundance_syl`: curated community ESV table from Sylvie


I formated the data.frame so that both of them have the following variables:

- `SampleID`: experiment ID used by Nanxi or Sylvie.
- `Community`: community, for instance, C2R4 or C1Rpool.
- `Transfer`: the transfer when the community was sequenced.
- `Adundance`: the number of this sequence in the community.
- `RelativeAbundance`
- `CommunityESVID`: the sequence identifier. This identifier is community-sequence specific.
- `ESV`: the DNA sequence in 16s V4 region.

In `communities_abundance_syl`, there are other parameters

- `CarbonSource`: the carbon source used for assembly
- `Order`, `Family`, and `Genus`: SILVA assigned taxonomy


```{r echo = T}
communities_abundance 
```


```{r echo = T}
communities_abundance_syl
```


Community richness along transfers based on `communities_abundance`

```{r}
communities_richness %>%
  group_by(Community, Transfer) %>%
  summarize(Richness = mean(Richness)) %>%
  ggplot(aes(col = Community, group = Community)) +
  geom_point(aes(x = Transfer, y = Richness)) +
  geom_line(aes(x = Transfer, y = Richness)) +
  scale_color_discrete() +
#  facet_wrap(Community~., scale = "free_y") +
  theme_bw()
```


```{r}
if (write_all_csv) {
  fwrite(communities_abundance, root$find_file("data/temp/communities_abundance.csv"))
  fwrite(communities_richness, root$find_file("data/temp/communities_richness.csv"))
  fwrite(communities_abundance_syl, root$find_file("data/temp/communities_abundance_syl.csv"))
}
```



# Match community ESVs and isolate Sanger sequences

```{r}
# It may take 10 mins
source("script/01E-match_community_abundance-02-match_isolate_16S.R")
```

Save the alignment result

```{r}
if (write_all_csv) {
#  fwrite(sequences_alignment, root$find_file("data/temp/sequences_alignment.csv")) 
  fwrite(sequences_alignment_syl, root$find_file("data/temp/sequences_alignment_syl.csv"))
}
```

IUPAC notation for DNA base pairs

W, S, M, K, R, Y represent two possiblities for one base pair
B, D, H, V represent three possiblitieis
N means any nucleotide (but not a gap)

I tested five alignment methods in `Biostrings::pairwiseAlignment()`

```{r}
alignment_type
```


```{r echo = T }
sequences_alignment_syl
```


```{r}
# R function for compute distinct Sanger
distinct_sanger <- function(x, allow_mismatch = 2) {
  sequences_alignment_syl %>%
    # Filter for BasePairMatch
    filter(BasePairMismatch <= allow_mismatch) %>%
    # For each Sanger, find the Sanger-ESV match with highest alignment score
    group_by(AlignmentType, ExpID) %>%
    arrange(desc(AlignmentScore)) %>%
    dplyr::slice(1) %>%
    ungroup() %>%
    # Remove duplicates that matches two Sangers to one ESV
    group_by(AlignmentType, Community, CommunityESVID) %>%
    distinct(RelativeAbundance, .keep_all = T) %>%
    arrange(Community) %>%
    # Specify mismatch allowed
    mutate(AllowMismatch = allow_mismatch) %>%
    group_by(AlignmentType) %>%
    summarize(Count = n())
}
```

Number of isolates being matched to the community ESV if we allow for up to two mismatches. 

```{r}
distinct_sanger(sequences_alignment_syl, allow_mismatch = 2)
```

Up to one mistmatch

```{r}
distinct_sanger(sequences_alignment_syl, allow_mismatch = 1)
```

No mistmatch

```{r}
distinct_sanger(sequences_alignment_syl, allow_mismatch = 0)
```


# Relative abundance explained by the sequences 

```{r message = F, warning = F}
source("script/01E-match_community_abundance-03-matched_abundance.R")
```

```{r}
if (write_all_csv) {
  fwrite(sequences_abundance, file = root$find_file("data/temp/sequences_abundance.csv"))
  fwrite(isolates_abundance, file = root$find_file("data/temp/isolates_abundance.csv"))
}
```


Abundances explained by ESVs

```{r}
communities_abundance_syl %>%
  filter(CarbonSource == "Glucose") %>%
  plot_abundance(label_x = "Community", label_y = "RelativeAbundance", fill = "Family")
```

Abundances explained by ESVs in 13 communties

```{r}
communities_abundance_syl %>% 
  filter(CarbonSource == "Glucose") %>% 
  filter(Community %in% communities_name) %>%
  plot_abundance(label_x = "Community", label_y = "RelativeAbundance", fill = "Family")
```


Abundance explained by isolate sequences, allowing up to two mismatch. 
C2R6 and C10R2 both miss one isolate's Sanger sequences.

```{r}
sequences_abundance %>%
  filter(AlignmentType == "local") %>%
  filter(AllowMismatch == 2) %>%
  mutate(AllowMismatch = paste0("AllowMismatch: ", AllowMismatch)) %>%
  plot_abundance(label_x = "Community", label_y = "RelativeAbundance", fill = "Family")
```

Abundance explained by isolate sequences. Rows are different alignment algorithms used by `Biostring::pairwiseAlignment()`, whereas columns are how many bp mismatches are allowed in ESV-Sanger matches. 

```{r fig.width=4, fig.height=4}
sequences_abundance %>%
  mutate(AllowMismatch = paste0("AllowMismatch: ", AllowMismatch)) %>%
  plot_abundance(label_x = "Community", label_y = "RelativeAbundance", fill = "Family") +
  facet_grid(AllowMismatch~AlignmentType) +
  theme(legend.position = "top")
```







